New sequencing technologies and increasingly dense SNP arrays are generating a flood of genetic data. Sample sizes are increasing and the spectrum of genotyped variation is broadening to include structural and multi-allelic variants. This research will develop improved genotype calling methods that are designed for these data and that use information from large sample sizes and from related individuals in novel and powerful ways. The result will be improved genotype data accuracy which will benefit all research on the genetic determinants of health and disease.